Related Experiment Video
Updated: Jun 26, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
DFT and docking analysis of stability, conformational dynamics, and interaction behavior in linear C6 triketo and
Atiyeh Kolouei1,2, Hamid Najarzadekan3, Mohammad Barati1
1Department of Applied Chemistry, Faculty of Chemistry, University of Kashan, Kashan, Iran.
Abstract:
Linear polycarbonyl motifs constitute flexible chemical frameworks with relevance to conformational analysis, molecular stability, and interaction modeling. Here, we report a combined density functional theory (DFT) and molecular docking study of the structural stability, conformational preferences, and interaction behavior of linear C₆ triketo and diketo scaffolds. Equilibrium geometries, intramolecular hydrogen-bonding patterns, and relative Gibbs free energies were evaluated at the B3LYP/6-311 + + G(d,p) level. Symmetric diketone isomers were identified as the most stable conformers, whereas arrangements containing adjacent carbonyl groups exhibited pronounced conformational flexibility accompanied by energetic destabilization of up to ~ 18 kcal mol⁻1. Across the scaffold series, a consistent instability window of ~ 12-16 kcal mol⁻1 was observed, associated with characteristic geometric distortions. To qualitatively probe interaction behavior, representative conformers spanning the stability range were subjected to molecular docking. Docking simulations were carried out against three key non-small cell lung cancer (NSCLC)-related targets, epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), and Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), to evaluate the biological relevance of the studied conformers and to relate conformational stability to binding behavior in a disease-relevant context. Energetically favorable conformers displayed well-defined and reproducible interaction poses, while less stable structures showed increased orientational variability consistent with their flexible potential energy surfaces.
Related Concept Videos
Stability of Substituted Cyclohexanes
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
Chair Conformation of Cyclohexane
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
Stability of Conjugated Dienes
A comparison of the enthalpies of hydrogenation of dienes reveals that conjugated dienes release less heat on hydrogenation, rendering them more stable than their nonconjugated analogs.
Conformations of Cyclohexane
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
Stereoisomerism of Cyclic Compounds
Newman Projections
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
